Phenolic compounds, carotenoids content (red and yellow), extractable colour (total pigments) and antioxidant activity in fruits from Chiltepin and Habanero pepper were investigated. The Habanero pepper had significantly higher total phenolic content (5.92 ± 0.47 mg/g GAE) than the Chiltepin pepper (4.85 ± 0.23 mg/g GAE). On the other hand, the highest content of total antioxidant activity was found in Chiltepin chili (11.10 ± 1.6 mg of GAE /g of dry weight). In contrast, Habanero chili showed the lowest values of total antioxidant activity. In this way, the Habanero chilli has the lowest content (14 mg/g dry weight) of carotenoids (yellow isochromic fraction) while the Chiltepin chilli had higher levels of yellow isochromic fraction (36 mg/g dry weigh). Finally, the Chiltepin showed the highest value ofextractable colour (80 ASTA units) than Habanero (40 ASTA units). Therefore Chiltepin and Habanero peppers are a good prospect for developing varieties with higher levels of bioactive compounds. Key words: Chiltepin pepper, Habanero pepper, phenolic compounds, carotenoids content, extractable colour, antioxidant activity.